Since UP Academy took over the Gavin Middle School in South Boston in 2011, some critics of charter schools have questioned whether the academy has been pushing out disruptive or academically struggling pupils in order to boost its test scores.

During the inaugural year of the in-district charter school, 19 percent of its pupils, 109 to be precise, left UP Academy. But that rate is slightly lower than the average for all the city’s middle schools, according to data compiled by the Boston School Department to dispel the notion that UP Academy is pushing out the worst pupils.

“The concept that our school is trying to push out students who are most challenging to serve is offensive,” said Scott Given, chief executive of ­Unlocking Potential, a Boston-based nonprofit that runs UP Academy. “Nothing could be further from the truth. Our ­organization’s mission is to ­successfully serve the most ­disadvantaged students in the city.”

Talk about UP Academy’s enrollment practices has been growing louder as the School Department prepares to let ­Unlocking Potential convert a second school into a charter school. Unlocking Potential specializes in turning around failing schools, and in just one year doubled the percentage of students scoring proficient and advanced at the former Gavin Middle School and secured double-digit increases in ­English scores on state exams.

The target of the latest venture is the Marshall Elementary School
in Dorchester, which would become UP Academy Charter School of Dorchester next fall, pending approval by the state Board of Elementary and Secondary Education.

Under the proposal, all ­pupils at the Marshall would be able to attend UP Academy so long as they fill out an application, a requirement of state law.

Still, critics and some school employees worry that Unlocking Potential will find a way to weed out the pupils most difficult to teach. They point out that 17 pupils at the Gavin who had multiple physical, cognitive, or other significant disabilities were barred from attending UP Academy.

In testimony to the Boston School Committee in October, Teresa Harvey-Jackson, the Marshall’s principal, who ­retired at the end of October, questioned whether all Marshall pupils would be welcomed at UP Academy and accused the School Department of cutting back enrollment of pupils with severe needs in anticipation of UP Academy’s arrival.

Matthew Wilder, a School Department spokesman, ­acknowledged enrollments of those pupils at Marshall are lower, but will probably increase.

Wilder also said that pupils with severe disabilities who attend­ed a specialized program at the Gavin were not enrolled at UP Academy because the School Department wanted to retain control of that program, rather than giving oversight to a private company. One concern was that the program could eventually fade away because new students admitted to UP Academy in future years would be subject to a lottery, which could result in no pupils with disabilities winning seats.

DAVID L. RYAN/GLOBE STAFF

Shelton Johnson (right) is among UP Academy’s pupils. Test scores have risen since it became a charter school.

Ultimately, of the pupils eligible to apply at the Gavin, 84 percent enrolled at UP Academy last fall. But as the year progressed, 44 of those former Gavin pupils left.

A few of those students landed at the McCormack Middle School in Dorchester. The pupils generally had discipline problems, and UP Academy drove one girl there while she was wearing her school uniform, said Paul Mahoney, dean of students at the McCormack.

“I know UP Academy is successful and God love them, but the bottom line is only a certain type of kid can go to school there,” Mahoney said. “We are a whole different world than UP Academy. We have to educate everyone.’’

Last year, the McCormack saw pupils withdraw at the same rate as UP Academy, 19 percent.

The reasons UP Academy pupils left last year are largely similar to those of pupils departing from other Boston middle schools, according to School Department data. Those figures include both the formed Gavin students at UP Academy and students new to the building last year, which includes the ­entire sixth-grade.

Some 42
pupils left because of “programmatic transfer,” a broad category that captures pupils who move to another city school for any number of reasons, such as families and pupils growing frustrated with the school, according to the School Department data. It was the top reason UP students left.

DAVID L. RYAN/GLOBE STAFF

Boston is preparing to let Unlocking Potential, which runs UP Academy, convert a second school into a charter school.

Some of the other reasons cited: 25 pupils moved out of the city, two were expelled, five transferred to other charter schools, six left for other public schools outside Boston (most likely through METCO), and 12 changed schools to get into a specific special education program.

Given stressed that UP Academy fights to keep every pupil and will match pupils with tutors or counselors and will even go to the mall to buy pupils an extra set of pants for their uniforms.

“I think for years critics of charter schools have tried to say that charter schools don’t serve the same students as district schools and that’s why we have been successful,” Given said. “Now UP Academy has delivered undeniable evidence that by utilizing practices of successful charter schools that students who have historically struggled within the district can succeed at high levels.’’